intron_sortseq

Analysis pipeline and downstream processing for study titled "Control of gene output by intron RNA structure". Includes processing of Sort-seq flow cytometry and sequencing data, as well as code to reproduce manuscript figures.

Installing the package

We used Snakemake with a custom conda environment. In addition, if you want to start from raw data, the following software packages need to be installed and accessible for Snakemake: fastp, bwa, Picard, LoFreq, samtools. Set the path to each software package in the config/snake_sort.yaml file.

# clone repository
git clone https://github.com/lschaerfen/intron_sortseq.git
cd intron_sortseq

# create conda environment
conda env create --name sort_env --file=sort_env.yml # create new environment from template
conda activate sort_env # activate

# install python package
pip install -e .

Re-generating analyses and figures from "Control of gene output by intronic RNA structure"

To re-generate the analyses, either run the analysis pipeline on deposited raw data, or download processed files from GEO accession number GSE308590. Save the raw or processed data files in the data directory in the respective folder. If starting from raw data, execute the Snakemake pipeline:

conda activate sort_env
snakemake -c 16 -d smk_rundir/run --configfile config/snake_sort.yaml

Analysis code for each individual figure is available in jupyter notebooks in the notebooks directory and can be executed directly using the processed data from GEO.